Clinical Research Data Warehouse

The CTSI’s Clinical Research Data Warehouse (CRDW) provides no-cost self-service tools to CITI-trained research teams for study feasibility, cohort discovery and data extraction. CRDW tools include the i2b2 Cohort Discovery Tool, TriNetX (a pharma-sponsored cohort query and analysis tool) and the Honest Broker data extraction tool.  Data sources include Epic, GE/IDX (physician billing system), Froedtert legacy systems (Affinity, Intellidose & SIS), MCW Tissue Bank biospecimens, NAACCR tumor registry, and genetic testing vendors (Foundation Medicine and Tempus).

The query tools help to answer the question “Does the CRDW contain a cohort of patients with certain characteristics?”

How to get access to the CRDW

CRDW Access Instructions

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Data Warehouse Workflow

Important Query Tool Notes

  • You don’t need an approved IRB protocol to use our query tools.
  • All data is de-identified.
  • All dates are shifted.
  • No names or IDs are available.

Query Concept Domains

The i2b2 query tool includes the following concept domains from which researchers can select criteria for cohort characterization.

  • Allergies
  • Biospecimens [Specimen Type, Tissue Site]
  • Custom Clinical Registries (e.g., AML/ALL Registry)
  • Clinical Trials [is the patient enrolled Y/N]
  • COVID Concepts [Diagnoses, Lab Results & Procedures]
  • Demographics [Age, Email, Ethnicity, Language, Race, Sex, Vital Status]
  • Diagnoses [ICD-9 & ICD-10]
  • Diagnostic Results [Clinical Labs, Cardiovascular/Pulmonary Diagnostics, Radiation]
  • Encounters (see Visit Details)
  • Genomics – genetic testing results from Foundation Medicine & Tempus
  • Immunizations
  • Medications [Ordered/Administered]
    • Pharmaceutical Class & Subclass
    • Ingredient
    • MAR Action, Route, Dose
    • Ordering Mode
  • NAACCR Tumor Registry from Froedtert Hospitals in Milwaukee, Menomonee Falls & West Bend
  • Procedures [CPT, HCPCS and custom codes from Epic Orders]
  • Procedures [CPT/HCPCS/ICD coding from Physician Billing & Hospital Billing]
  • Providers (searchable by name and specialty)
  • Social History [Alcohol, Contraceptives, Illicit Drug Use, Tobacco Use, SDOH]
  • Visit Details
    • Age at Visit
    • Department
    • Visit Type (e.g., AV=ambulatory, IP=inpatient)
  • Visit Vitals (outpatient only)

The TriNetX query tool includes Demographics, Medications, Diagnoses, Diagnostic Testing Results, Procedures and Genomics.

Data Contributors

  • Froedtert Health System (FH): includes Froedtert Milwaukee Hospital, Froedtert Menomonee Falls Hospital (Community Memorial Hospital), Froedtert West Bend Hospital (St. Joseph’s Hospital West Bend), Community Physicians clinics, and Medical College of Wisconsin clinics
  • Children’s Hospital of Wisconsin (CHW): includes Children’s Specialty Group physician data

Terms of Use

Terms of Use

Users of the Clinical Research Data Warehouse acknowledge that:

  • This system was not designed, nor is it intended, to support any aspect of patient care and its use for any patient care purposes is prohibited.
  • The results returned by this system may not be distributed outside of Medical College of Wisconsin.
  • All searches executed within the system are recorded and will be examined, as part of routine compliance audits. The identity of the user is recorded along with information related to each search executed.
  • No person registered as a user of the system may share his/her login information with any other person for purposes of accessing this system. Only registered users who are Medical College of Wisconsin faculty, adjunct faculty, or academic staff may use the system.

Requirements

Requirements

To use the Medical College of Wisconsin’s Clinical & Translational Research Informatics tools you must:

  • Be a MCW faculty or adjunct faculty or sponsored by either one
  • Have credentials to access the Medical College of Wisconsin network (facilitated by a CTSI business analyst)
  • Have access to the MCW Citrix portal ( mycitrix.mcw.edu ) which requires a local download of Citrix
  • Have access to MCW’s multi-factor authentication application (currently Duo)

Prerequisites to access the Clinical Research Data Warehouse tools

  • CTSI membership
  • Current MCW-required Human Subjects Research CITI Training
  • CRDW Data Release Agreement from the project PI with all research team members listed on the Project Team form

Language to Include in IRB Applications

Language to Include in IRB Applications

TEMPLATE LANGUAGE FOR INVESTIGATORS USING MCW CLINICAL RESEARCH DATA WAREHOUSE (CRDW) – FOR USE IN MCW IRB APPLICATIONS

FOR ALL 5 SCENARIOS BELOW: Investigators that MIGHT utilize CRDW data MUST link their eBridge study applications to the CRDW bank (PRO00013874) in Section 26 of the SmartForm.

Please explain your use of the CRDW using the following templated language within the indicated sections of the IRB application SmartForm… otherwise the IRB will not understand what you are doing and the review of your application, as well as the approval of your data request(s), will be delayed.

I. FOR INVESTIGATORS USING THE CRDW TO IDENTIFY AND/OR CONTACT ELIGIBLE PARTICIPANTS

In the Recruitment section (17.2) of SmartForm, the investigator should check Other Strategies and clearly state how CRDW tools may be used to identify potential participants and gain access to their contact information.

The investigator should state:

“To identify potential participants and obtain their contact information for recruitment, the investigator will (a) search for eligible participants with the following inclusion/exclusion criteria by querying a cohort discovery tool (i2b2 and/or TriNetX) from the MCW Clinical Research Data Warehouse (PRO00013874) , and then (b) seek IRB approval to extract the following contact information for each identified potential participant using the Honest Broker tool:

  1. <Specify cohort inclusion/exclusion criteria to be queried>
  2. <Specify participant contact information to be extracted>
Using this contact information, the investigator will then…”

II. FOR INVESTIGATORS USING THE CRDW TO ACCESS IDENTIFIED DATA WITH OR WITHOUT PARTICIPANT RECRUITMENT

In the Protocol Summary (19.7) or Procedures (30.1) section of the SmartForm, the investigator must clearly state whether the CRDW is the ONLY way potential participants will be identified or the CRDW is ONE OF SEVERAL participant identification strategies.

The investigator should state:

“Clinical data for this study will be obtained by… <indicate one of the following options>

  1. …searching for eligible participants by querying a cohort discovery tool (i2b2 and/or TriNetX) from the MCW Clinical Research Data Warehouse (PRO00013874) with (a) the following inclusion/exclusion criteria, and (b) seeking IRB approval to extract or access the following clinical information for each identified participant using the Honest Broker tool:
    1. <Specify cohort inclusion/exclusion criteria to be queried>
    2. <Specify clinical information to be extracted/accessed>
  2. …entering a list of medical record numbers for identified participants into the Honest Broker tool and then submitting an approval request to the IRB for the following clinical information for each participant:
    1. <Specify clinical information to be extracted/accessed>
Using this identified clinical information, the investigator will then…”

III. FOR INVESTIGATORS USING THE CRDW TO ACCESS FULLY DE-IDENTIFIED DATA OR A LIMITED DATA SET for purposes other than participant recruitment

**Some investigators may not be required to submit anything to the IRB for this scenario – contact CRDW.mcw.edu for guidance. Other investigators may have “mixed” projects involving CRDW de-identified data AND other activities requiring IRB review.**

In the Protocol Summary (19.7) or Procedures (30.1) section of the SmartForm, the investigator must clearly state whether the CRDW is the ONLY way potential participants will be identified or the CRDW is ONE OF SEVERAL participant identification strategies.

The investigator should state:

“Clinical data for this study will be obtained by searching for eligible anonymous participants using a cohort discovery tool (i2b2 and/or TriNetX) from the MCW Clinical Research Data Warehouse (PRO00013874) with (a) the following inclusion/exclusion criteria, and then (b) extracting the following de-identified clinical information for each identified participant:

  1. <Specify cohort inclusion/exclusion criteria to be queried>
  2. <Specify clinical information to be extracted>
Using this de-identified clinical information, the investigator will then…”

IV. IMAGE DE-IDENTIFICATON (the most typical situation) the investigator has IRB approval to access identified F&MCW images, but wants them de-identified so the images can be sent outside F&MCW in de-identified format

The investigator should “prove up” to the CRDW gateway that the investigator already has IRB approval to access or use these specific images, and IRB approval for access to IDENTIFIED images. When in doubt, the CRDW can and should always check with an IRB staff person.

The investigator wants to send a scan image to an external party (sponsor, collaborator) de-identified because the STUDY PROTOCOL requires de-identification in this situation, and/or the IRB APPLICATION promised de-identification in this situation, and/or the STUDY CONSENT FORM promised de-identification in this situation. Thus — even though scrutiny of the HIPAA authorization language may show that the participant has in general authorized the investigator to share some identified information with the third party — de-identification of the image scan is still REQUIRED.

In the Procedures section (30.1) of SmartForm, the investigator should state in the IRB application:

“Identified scan images to be provided to XXX and YYY (external third parties) will be totally de-identified per study protocol by submitting index images and destinations to the Honest Broker / Image De-Identification Service of the MCW Clinical Research Data Warehouse and having that Honest Broker send the de-identified images.” [Though it may be clear elsewhere in the protocol, the PI should again state here what kinds of images and how many images will be sent this way.]

V. IMAGE DE-IDENTIFICATION (less common situation) where the investigator wants to use a CRDW cohort discovery tool (i2b2 and/or TriNetX) to identify eligible participants and then have the CRDW deliver de-identified images for that cohort, so the activity (on the part of the PI receiving de-identified images from a valid honest broker) does not technically qualify as “human subjects research.”

In the Procedures section (30.1) of SmartForm, the investigator must clearly state whether the CRDW is the ONLY way potential participants will be identified or the CRDW is one of several participant identification strategies.

The investigator should state in the IRB application:

“Clinical data for this study will be obtained by using a cohort discovery tool (i2b2 and/or TriNetX) from the MCW Clinical Research Data Warehouse (PRO00013874), to (a) search for eligible participants with the following inclusion/exclusion criteria, and then (b) seek IRB approval for this project asking the CRDW to provide the following clinical information and SCANS for each identified participant:

  1. <Specify cohort inclusion/exclusion criteria to be queried>
  2. <Specify clinical information to be extracted>

 

Note: this method of accessing de-identified data may ultimately be deemed “not human subjects research” depending on what else the investigator will be doing.

Download this Information
Citation Information

Citing the Clinical Research Data Warehouse

Investigators must cite both AHW and Medical College of Wisconsin CTSA Grant UL1TR001436.

This includes use of the self-service cohort discovery tool, data consultations, clinical queries, and data extraction services made by our team.

AHW

“This project is funded in part by the Advancing a Healthier Wisconsin endowment at the Medical College of Wisconsin.”

CTSA

Please acknowledge the Medical College of Wisconsin CTSA Grant UL1TR001436. All publications must comply with NIH Public Access Policy.

Researchers other than K Scholars (KL2) – Please cite Grant UL1TR001436, as follows:
“This publication [or project] was supported by the National Center for Research Resources and the National Center for Advancing Translational Sciences, National Institutes of Health, through Grant Number UL1TR001436. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH.”
K Scholars (KL2) – Please cite Grant KL2TR001438, as follows:
“This publication [or project] was supported by the National Center for Research Resources, the National Center for Advancing Translational Sciences, and the Office of the Director, National Institutes of Health, through Grant Numbers  UL1TR001436 and KL2TR001438. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH.”
Fees

Fees / Cost Structure Notice

Project Inclusions

Each project includes the following training and support:

  • 1 hour training (no charge)
  • 1 hour project support (no charge)

Any project scope expansion beyond the included 2 hours, as outlined above, is considered out of scope and may affect your data delivery timeline and/or budget.

Additional Support

Additional project support is billed hourly at a rate of $90 per hour ($100/hr effective 7/1/2017). No work on scope changes will be done before both parties agree on cost and timeline changes and are client authorized with approval of a written change order.

Fees last updated June 30, 2017
What do I need to do if I want to…?

What do I need to do if I want to…?

Validate a research hypothesis by generating a de-identified cohort

No IRB review required.

Test a QA/QI hypothesis by generating a de-identified cohort

No IRB review required.

Extract de-identified data from Honest Broker for a known cohort or a cohort generated from a query tool such as i2b2 or TriNetX

No IRB review required.

Extract data from Honest Broker for a known cohort or an identified cohort generated using a query tool such as i2b2 or TriNetX

IRB approval required.

Extract data from Honest Broker for a known cohort or an identified cohort generated through i2b2 for QA/QI

  • Contact your Department Administrator and/or the MCW IRB
  • Working on processes for CHW

Access Form

CRDW Data Release Agreement (Access to all query and data extract tools)

De-Identified Data Query & Extraction

Research teams may use the CRDW’s self-service de-identified cohort discovery query tools to curate and iteratively refine cohorts for hypothesis development. Researcher teams may also extract and review de-identified clinical data as a preliminary step before requesting identified data for a research project.

The CTSI Biomedical Informatics team will provide up to 2 hours of complimentary consultation and training to develop queries and/or extracts that meet the specific needs of each research project.

Research teams should define specific inclusion and/or exclusion criteria to build a study cohort within one of the CRDW query tools. This curated cohort can then be used to export various data tables from the Honest Broker extract tool in CSV format. CSV files are compatible for import into many data analysis tools.

De-Identified data extracts should be treated as if they contain real patient data – they must be stored on a secure device or network drive.

Teams who wish to identify the patients in their cohort must apply to the IRB for study approval in order to extract identified patient data.

Identified Data Extraction Requires IRB Approval

Research projects wanting to use identified data or a limited data set must have an approved IRB protocol to extract identified data from Honest Broker. Project teams are encouraged to use the de-identified query tools to inform protocol content, i.e. validating the cohort size for Section 3F.

Simply receiving IRB approval does not guaranty Honest Broker approval. There are 5 IRB checkpoints that must be in place on the eBridge SmartForm for a successful Honest Broker submission: Sections 2.1 (team members), 3F (both dates and counts), 19.7/30.1 (process language), and 26.2 (link to CRDW bank).

Existing protocols should be reviewed to ensure all IRB checkpoints are covered. In some cases, the researcher must submit an IRB amendment to include additional elements and/or language. To request a protocol review, please contact CRDW@mcw.edu.

DATA ANALYSIS

The Medical College of Wisconsin’s Clinical & Translational Research Informatics team offers a number of research data management options in support of clinical research, including: REDCap, and Secure ResearchWiki. We strongly encourage researchers to consult with a biostatistician from the CTSI, CAPS, or MCW’s Institute for Health & Society before beginning the analysis of their clinical data.

COST

Inquiries and consultations on new research projects are offered free of charge to CTSI community researchers. In general, we will provide one hour of labor working on a project before we need to discuss setting up a payment plan.

When additional payment is required, you will be responsible for covering a standard billing rate on an hourly basis for the time spent working on your project.

In projects where Biomedical Informatics expertise is required, we may engage in a collaborative partnership leading to co-authorship on related publications. In such a collaboration, and particularly where the work is of shared interest, we may be able to extend a cost-sharing of services.

Citation

We ask that all research related to your consultation include appropriate citations to the resources used. Please see our citation information for details.

CRDW Data Release Agreement

To gain access to the Clinical Research Data Warehouse, a PI must complete the following form. The PI must be a registered CTSI member and be designated as Faculty or Adjunct Faculty. In order to grant access to research team members, the PI must provide a name, contact information and project role for each team member on the Project Team form.

Only MCW employees/students/adjunct faculty or CTSI community partners with an MCW Network ID (e.g., an @mcw.edu email address) can be given access to the CRDW.